SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2347 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but s...2258 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to jo...repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2250 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensit...ign the reads, including those spanning (complex) structural variations. Ngmlr uses an SV...tifying the position of breakpoints stemming from structu...2215 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologie...Flye performs an extra repeat classification and analysis step to improve the structu...2206 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer...p for microbial datasets. In real-time mode, it can be integrated with simple structu...2168 days ago
2167 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...s using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 1...2195 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yie...ots, along with the positions, sequence, and flanking base pairs of each such structu...2187 days ago
2182 days ago